Vaccine and biotech stocks plunged after a top regulator left the US Food and Drug Administration, casting deep uncertainty about the future of vaccines and cutting-edge gene therapies.

Peter Marks, a key figure overseeing the review and approval of vaccines and other medications, resigned on Friday, citing friction with the views of new Health and Human Services Secretary and longtime vaccine critic Robert F. Kennedy Jr.

Marks told peers that he was asked on the spot to decide whether to step down or be fired, according to people familiar with the discussions.

“Peter Marks has been pushed out,” Cantor analyst Josh Schimmer wrote in a note that summed up the feeling of many observers. “OMG. Not good.”

The departure of Marks from the FDA’s Center for Biologics Evaluation and Research raised red flags for industry leaders, Wall Street analysts and former health officials, who said they were worried about the politicization of the scientific process and whether other experienced health officials might also be forced out.

The change also creates uncertainty for the highly-regulated pharmaceutical industry.

Moderna Inc. shares fell as much as 14% in Monday trading, while the SPDR S&P Biotech ETF lost as much as 6%. Other makers of vaccines and drugs like gene therapies saw their stocks drop, including Novavax Inc., BioNTech SE and Sarepta Therapeutics Inc.

In his resignation letter, Marks said that he had been willing to work with Kennedy to “address the Secretary’s concerns regarding vaccine safety and transparency.”

“However it has become clear that truth and transparency are not desired by the Secretary, but rather he wishes subservient confirmation of his misinformation and lies,” Marks said.

The change is a “significant negative” for biotech and biopharma, which depend on independence and scientific rigor at FDA, BMO Capital Markets analyst Evan David Seigerman said in a note.

“While we are positive on the confirmation of Dr. Marty Makary as FDA commissioner, antiscience, politicization of FDA runs counter to the agency’s mission,” he said.

Marks did not return requests for comment.

A physician who previously worked in the pharmaceutical industry and as a Yale University academic, Marks joined the FDA in 2012. He had been the director of CBER for nearly a decade and played a key role in quick approvals of Covid vaccines during the pandemic.

His departure represents “the loss of experienced leadership at the FDA” and the biotech industry is deeply concerned that “will erode scientific standards and broadly impact the development of new, transformative therapies to fight diseases for the American people,” John Crowley, CEO of the biotech industry group BIO, said.

In a social media post, former FDA Commissioner Robert Califf — who Marks worked for — said the former CBER director’s description of conflict with Kennedy over vaccine misinformation “should be frightening to anyone committed to the importance of evidence to guide policies and patient decisions.”

Moncef Slaoui, a biotech venture capitalist and former scientific head of Operation Warp Speed, said Marks’ departure was unfortunate for the agency because he had been on the forefront of regulating vaccines, biologics and groundbreaking cell and gene therapies.

“My take from Peter is he is a science-driven regulator instead of a process-driven regulator, and that’s how progress has been made... It’s important for regulators to be endorsing innovation and change,” Slaoui said.

In addition to his role during Covid, Marks became known for championing a faster and more flexible approach to approving new treatments for rare diseases, especially genetic medicines that aim to cure disorders in as little as one dose.

But critics of Marks have said he’s been too friendly to the pharmaceutical industry and ignored advice of top vaccine scientists and outside experts during the Covid pandemic.

Incoming FDA Commissioner Makary had faulted the agency for declining to seek input from outside experts on whether young people should get Covid vaccine boosters. Two vaccine scientists left due to disagreements with Marks during reviews of Covid boosters.

‘Greatest Advocate’

Marks’ tenure at FDA had been controversial in other ways. Last year, he supported expanded approval of Sarepta’s gene therapy for Duchenne muscular dystrophy, even though it failed to clearly slow the overall disease in multiple trials and two FDA reviewers recommended against it. RBC Capital Markets analyst Brian Abrahams cited Marks’ departure as one reason why he was downgrading Sarepta’s stock on Monday, saying it “adds greater regulatory uncertainty.”

With Sarepta’s “greatest advocate” now gone, “we could see additional risks of stricter warnings around the gene therapy product,” he said.

Kennedy’s stance on vaccines has already begun shaping the government’s approach to public health. Bloomberg reported last week on leaked documents that describe a Trump administration plan to cut almost $28 billion in global health initiatives. The cuts include funds for Gavi, a vaccine alliance that immunizes millions of children against deadly diseases. HHS also has been reviewing funding for Moderna’s development of a vaccine against H5N1 bird flu as an outbreak among birds and cattle has hit multiple states.

Amid a deadly outbreak of measles in Texas, the health secretary has stressed that highly effective vaccines against the disease are a personal choice, and said that high doses of vitamin A can also be effective. Media outlets have reported that several children have been hospitalized in the state due to liver toxicity from high doses of the vitamin.

--With assistance from Madison Muller.